Re: TM protein in octane slab questions

From: Richard Law (
Date: Fri Jul 22 2005 - 12:30:54 CDT

I think the only reason Gromacs is used more for octane simulations that
NAMD is simply because Peter Tieleman, who was involved in the development
of Gromacs, favored this media over lipid due to the faster relaxation
time. Subsequently there were several papers from the Sansom group, where
Peter post-doc-ed for a bit. Added to that the fact that it's not
standard in the Charmm topology.

Yes you only need to modify the topology file unless you create any new
atoms. It should be relatively straight forward, especially since hexane
is there.


On Fri, 22 Jul 2005, Michel Seigneuret wrote:

> Dear Namd users,
> I would like to do some MD on a transmembrane protein with Namd
> using an octane slab with water (due to limited computational resources).
> Here are a few questions:
> 1) While there are many publications doing this with full phospholipids
> using either Namd or Gromacs, most publications with octane use Gromacs
> ( I found only one octane work with Namd). Is there a reason why Gromacs
> should be better for octane slabs ? I would prefer to use Namd since I have
> some
> (limited) experience with it.
> 2) Strangely, there are RESI entries for hexane in top_all27_prot_lipid.inp
> (although not in all versions I found) but not for octane. There is an
> octane entry in
> toprna10r_22.inp but the atom type nomenclature is different. Does somebody
> have or know of consistent CHARMM topology or parameter files that include
> octane? If not, is it feasible for a semi-beginner to write an octane entry
> ? Am I
> correct in assuming that only the topology file would have to be modified,
> not the
> parameter file.
> Thanks in advance for your help.
> Michel
> Michel Seigneuret
> Institut Cochin, U567-UMR8104
> Département de Biologie Cellulaire
> 22 rue Méchain, 75014 Paris, France
> Tel: 33 (0)1 40 51 64 50
> Fax: 33 (0)1 40 51 64 54

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